[Biopython] interactive shell to use with biopython?

[Björn Johansson]

Thank you for the tip, iPython seems very useful as it works the sam way as
the normal python interpreter. The notebook looks impressive, I will give
it a try when the ipython 0.13 comes out.

/bjorn


On Tue, Apr 17, 2012 at 08:42, Andrew Perry <ajperry at pansapiens.com> wrote:

> On Tue, Apr 17, 2012 at 4:44 PM, Björn Johansson <
> bjorn_johansson at bio.uminho.pt> wrote:
>
>> Hi all,
>>
>> I would like to know what interactive shell might be a good
>> alternative to use with biopython.
>> Ideally, it should be possible to save interactive commands and save
>> them to run later.
>>
>> Could you give me some examples of what youa are using?
>>
>> Thanks,
>> Bjorn
>>
>>
> You might want to check out iPython in notebook mode. I've only played
> with it briefly, but it looks promising for interactive analysis, and cases
> where you'd like to present the transcript to others.
>
> 'Regular' commandline iPython will also allow you to save the history with
> the %save command.
>
> See: http://ipython.org/ipython-doc/stable/interactive/htmlnotebook.html
>
> To get an idea of how it works, see Titus Brown's demonstration:
> http://www.youtube.com/watch?feature=player_detailpage&v=HaS4NXxL5Qc#t=132s
>
> Andrew Perry
>
> Postdoctoral Fellow
> Whisstock Lab
> Department of Biochemistry and Molecular Biology
> Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia.
> Mobile: +61 409 808 529
>
>


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